Each has it's benefits, personally I fly mode two as I'm more of a heli guy, and for how heli's fly in a hover and landing etc, I can see and feel when I'm flying just how it makes more sense - plane's cannot just go sideways all of a sudden from a stationary point in the sky.
As for planks (which I have now as well), I can see how mode one would be better as you can separate elevator and aileron much easier re fine tuning a banked turn etc when referring to general sport type flying (for a noob it takes some thumb skill to add elevator when turning/banking a plane in mode 2 being it's all down to controlling one little stick while your eyes are elsewhere, personally I'm thankful for the high quality simulators we have now days!).

At the local field where I go, the majority of heli guys fly mode 2, while the majority of plane guys fly mode 1 - that said, there are exceptions, and that is normally when a specific pilot has come from starting their hobby life in the other camp (where I fly, all mode 1 heli guys started of with planks for example).

At the end of the day, does it really matter? .... if starting out, take into account what the local guys at your club use, and fly whatever mode makes the most sense to you after taking into account all the factors relating to YOU. Also, learn on a sim to get thumb memory and general flight 'physic' characteristic's when starting out (it will save you serious money when you invest into a good high end sim like Phoenix/Realflight etc), then just get out and just have fun taking to the air!

(I added the learning comments as those in to hobby already will have long since made their mind up, and not a lot we say in here will effect that! (noobs on the other hand can be led through personal views being misunderstood as fact or best practice)